Confocal Stereology - 3D Volumetric Measurement - Reply to Earl Stanford

[Won Yung Choi, Ph.D.]

*****Commercial Announcement Regarding Confocal Stereology ******

This is a response to Earl Stanford's question regarding 3-D volumetric
measurements and as this has an aspect of commercial announcement (as well
as scientific content), I've started a new thread.

I am a product scientist specializing in stereology solution for Visiopharm,
and I would like to let you know that Visiopharm can integrate to confocal
microscopes for true stereological quantification that uses systematic
uniform random sampling in selection of the fields of view to quantify from.
 Using stereology, one can obtain unbiased estimation of the structure of
interest (e.g. volume, length, count, surface area, local volume and cross
sectional area estimation) and many journals now require stereological
quantification for brightfield and widefield microscopy.  

At the moment, no journal that I know of requires this for confocal
microscopes as not many people have been aware of the fact that one can
indeed perform confocal stereology.  By this, what we mean is a bona fide
method of sampling from correct fields by controlling the stage position
from the stereology software in a systematic uniform random manner.  This
does not mean that the user is choosing the field of view to quantify from,
capturing images, then plugging these images to a stereology package.  This
latter approach introduces sampling bias, and is not a valid method of
performing stereological quantification.  As a growing number of scientists
are aware of the importance of stereological sampling, the number of labs
using confocal stereology is growing and the trend for publication
requirements will certainly follow.  

Stereological quantification is differentiated from volume rendering or
other exhausitive quantification method in that one can sample to make the
quantificaiton process much more efficient while being completely unbiased
with no assumptions regarding the shape, size and orientation of the
structure of interest.  

I personally have used Zeiss LSM510 extensively as a postdoc and I was
unable to perform stereological quantification for my studies as confocal
stereology tool was not yet available.  I sincerely hope that many
scientists reading this become aware of the ability to perform true confocal
stereology and  can take advantage of these latest technological advances.

At the moment, Visiopharm can integrate to Zeiss LSM 510 and 710, Leica,
Olympus DSU, and are in development to integrate to several other confocals
currently out in the market today.  Please contact me at [hidden email]
for further information.  Thank you.

[kubinova]

Dear all,

My lab has been involved in methods of "confocal stereology" and
comparisons of different stereological and image analysis methods (such as
those applied to binary 3D images obtained by image segmentation) since
early nineties, including methods for volume measurement. Maybe it would
be of interest for you to have a look at some of our papers on this topic
listed below (available from me, [hidden email], or Jiri Janacek,
[hidden email], on request).
As to software, at present we are using our own software modules for
stereology and image analysis(available for free) running in Ellipse
program (ViDiTo, Kosice, Slovakia; not for free; commercial interest) -
see http://www.ellipse.sk/

Selection of our papers on volumetric and other measurements based on 3D
image data:
1. Kubinova, L., Janacek, J., Guilak, F., Opatrny, Z.: Comparison of
several digital and stereological methods for estimating surface area and
volume of cells studied by confocal microscopy. Cytometry 36: 85-95, 1999.
2. Kubinova, L., Janacek, J.: Confocal microscopy and stereology:
Estimating volume, number, surface area and length by virtual test probes
applied to three-dimensional images. Microsc. Res. Techn. 53: 425-435,
2001.
3. Kubinova, L., Janacek, J., Krekule, I.: Stereological methods for
estimating geometrical parameters of microscopical structure studied by
three-dimensional microscopical techniques. In: A.Diaspro (Ed.): Confocal
and Two-photon Microscopy: 299-332, Wiley-Liss, New York, 2002.
4. Kubinova, L., Janacek, J., Karen, P., Radochova, B., Difato, F.,
Krekule, I.: Confocal stereology and image analysis: Methods for
estimating geometrical characteristics of cells and tissues from
three-dimensional confocal images. Physiol. Res. 53 (Suppl.1): S47-S55 ,
2004.
5. Difato, F., Mazzone, F., Scaglione, S., Fato, M., Beltrame, F.,
Kubinova, L., Janacek, J., Ramoino, P., Vicidomini, G., Diaspro, A.:
Improvement in volume estimation from confocal sections after image
deconvolution. Microsc. Res. Techn. 64: 151-155, 2004.
6. Kubinova L., Janacek, J., Albrechtova, J., Karen, P.: Stereological and
digital methods for estimating geometrical characteristics of biological
structures using confocal microscopy. In: Evangelista, V.; Barsanti, L.;
Passarelli, V.; Gualtieri, P. (Eds): From Cells to Proteins: Imaging
Nature across Dimensions. NATO Security Through Science Series, Sub-Series
B: Physics and Biophysics, Vol. 3, Springer, 2005, pp. 271-321.
7. Cebasek, V., Erzen, I., Vyhnal, A., Janacek, J., Ribaric, S., Kubinova,
L.: The estimation error of skeletal muscle capillary supply is
significantly reduced by 3D method. Microvasc. Res. 79(1): 40-46, 2010.

Please, do not hesitate to contact us for further information.

Best wishes,

Lucie
_____________________________________________________________
Lucie Kubinova, PhD.
Director
Institute of Physiology ASCR
Videnska 1083
CZ-14220
Prague 4
Czech Republic
E-mail: [hidden email]

> *****Commercial Announcement Regarding Confocal Stereology ******
>
> This is a response to Earl Stanford's question regarding 3-D volumetric
> measurements and as this has an aspect of commercial announcement (as well
> as scientific content), I've started a new thread.
>
> I am a product scientist specializing in stereology solution for
> Visiopharm,
> and I would like to let you know that Visiopharm can integrate to confocal
> microscopes for true stereological quantification that uses systematic
> uniform random sampling in selection of the fields of view to quantify
> from.
>  Using stereology, one can obtain unbiased estimation of the structure of
> interest (e.g. volume, length, count, surface area, local volume and cross
> sectional area estimation) and many journals now require stereological
> quantification for brightfield and widefield microscopy.
>
> At the moment, no journal that I know of requires this for confocal
> microscopes as not many people have been aware of the fact that one can
> indeed perform confocal stereology.  By this, what we mean is a bona fide
> method of sampling from correct fields by controlling the stage position
> from the stereology software in a systematic uniform random manner.  This
> does not mean that the user is choosing the field of view to quantify
> from,
> capturing images, then plugging these images to a stereology package.
> This
> latter approach introduces sampling bias, and is not a valid method of
> performing stereological quantification.  As a growing number of
> scientists
> are aware of the importance of stereological sampling, the number of labs
> using confocal stereology is growing and the trend for publication
> requirements will certainly follow.
>
> Stereological quantification is differentiated from volume rendering or
> other exhausitive quantification method in that one can sample to make the
> quantificaiton process much more efficient while being completely unbiased
> with no assumptions regarding the shape, size and orientation of the
> structure of interest.
>
> I personally have used Zeiss LSM510 extensively as a postdoc and I was
> unable to perform stereological quantification for my studies as confocal
> stereology tool was not yet available.  I sincerely hope that many
> scientists reading this become aware of the ability to perform true
> confocal
> stereology and  can take advantage of these latest technological advances.
>
> At the moment, Visiopharm can integrate to Zeiss LSM 510 and 710, Leica,
> Olympus DSU, and are in development to integrate to several other
> confocals
> currently out in the market today.  Please contact me at
> [hidden email]
> for further information.  Thank you.
>

[James Ackman-2]

"Won Yung Choi, Ph.D." <[hidden email]> wrote:

>*****Commercial Announcement Regarding Confocal Stereology ******
>
>This is a response to Earl Stanford's question regarding 3-D volumetric
>measurements and as this has an aspect of commercial announcement (as well
>as scientific content), I've started a new thread.
>
>I am a product scientist specializing in stereology solution for Visiopharm,
>and I would like to let you know that Visiopharm can integrate to confocal
>microscopes for true stereological quantification that uses systematic
>uniform random sampling in selection of the fields of view to quantify from.
> Using stereology, one can obtain unbiased estimation of the structure of
>interest (e.g. volume, length, count, surface area, local volume and cross
>sectional area estimation) and many journals now require stereological
>quantification for brightfield and widefield microscopy.  
>
>At the moment, no journal that I know of requires this for confocal
>microscopes as not many people have been aware of the fact that one can
>indeed perform confocal stereology.  By this, what we mean is a bona fide
>method of sampling from correct fields by controlling the stage position
>from the stereology software in a systematic uniform random manner.  This
>does not mean that the user is choosing the field of view to quantify from,
>capturing images, then plugging these images to a stereology package.  This
>latter approach introduces sampling bias, and is not a valid method of
>performing stereological quantification.  As a growing number of scientists
>are aware of the importance of stereological sampling, the number of labs
>using confocal stereology is growing and the trend for publication
>requirements will certainly follow.  
>
>Stereological quantification is differentiated from volume rendering or
>other exhausitive quantification method in that one can sample to make the
>quantificaiton process much more efficient while being completely unbiased
>with no assumptions regarding the shape, size and orientation of the
>structure of interest.  
>
>I personally have used Zeiss LSM510 extensively as a postdoc and I was
>unable to perform stereological quantification for my studies as confocal
>stereology tool was not yet available.  I sincerely hope that many
>scientists reading this become aware of the ability to perform true confocal
>stereology and  can take advantage of these latest technological advances.
>
>At the moment, Visiopharm can integrate to Zeiss LSM 510 and 710, Leica,
>Olympus DSU, and are in development to integrate to several other confocals
>currently out in the market today.  Please contact me at [hidden email]
>for further information.  Thank you.

[James Ackman-2]

Reeuewqwqsqqqrqqqq&37321$31131,4111111111,11412141uquqqqqq34711153711121q41121q71&$111211$1717qq??wqqqqrs, 311qweeqqwq

"Won Yung Choi, Ph.D." <[hidden email]> wrote:

>*****Commercial Announcement Regarding Confocal Stereology ******
>
>This is a response to Earl Stanford's question regarding 3-D volumetric
>measurements and as this has an aspect of commercial announcement (as well
>as scientific content), I've started a new thread.
>
>I am a product scientist specializing in stereology solution for Visiopharm,
>and I would like to let you know that Visiopharm can integrate to confocal
>microscopes for true stereological quantification that uses systematic
>uniform random sampling in selection of the fields of view to quantify from.
> Using stereology, one can obtain unbiased estimation of the structure of
>interest (e.g. volume, length, count, surface area, local volume and cross
>sectional area estimation) and many journals now require stereological
>quantification for brightfield and widefield microscopy.  
>
>At the moment, no journal that I know of requires this for confocal
>microscopes as not many people have been aware of the fact that one can
>indeed perform confocal stereology.  By this, what we mean is a bona fide
>method of sampling from correct fields by controlling the stage position
>from the stereology software in a systematic uniform random manner.  This
>does not mean that the user is choosing the field of view to quantify from,
>capturing images, then plugging these images to a stereology package.  This
>latter approach introduces sampling bias, and is not a valid method of
>performing stereological quantification.  As a growing number of scientists
>are aware of the importance of stereological sampling, the number of labs
>using confocal stereology is growing and the trend for publication
>requirements will certainly follow.  
>
>Stereological quantification is differentiated from volume rendering or
>other exhausitive quantification method in that one can sample to make the
>quantificaiton process much more efficient while being completely unbiased
>with no assumptions regarding the shape, size and orientation of the
>structure of interest.  
>
>I personally have used Zeiss LSM510 extensively as a postdoc and I was
>unable to perform stereological quantification for my studies as confocal
>stereology tool was not yet available.  I sincerely hope that many
>scientists reading this become aware of the ability to perform true confocal
>stereology and  can take advantage of these latest technological advances.
>
>At the moment, Visiopharm can integrate to Zeiss LSM 510 and 710, Leica,
>Olympus DSU, and are in development to integrate to several other confocals
>currently out in the market today.  Please contact me at [hidden email]
>for further information.  Thank you.